494 lines
14 KiB
C++
494 lines
14 KiB
C++
/*Copyright (c) 2012 The Broad Institute
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*Permission is hereby granted, free of charge, to any person
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*obtaining a copy of this software and associated documentation
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*files (the "Software"), to deal in the Software without
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*restriction, including without limitation the rights to use,
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*copy, modify, merge, publish, distribute, sublicense, and/or sell
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*copies of the Software, and to permit persons to whom the
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*Software is furnished to do so, subject to the following
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*conditions:
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*The above copyright notice and this permission notice shall be
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*included in all copies or substantial portions of the Software.
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*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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#include "headers.h"
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#include "template.h"
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#include "utils.h"
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#include "vector_defs.h"
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#include "LoadTimeInitializer.h"
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using namespace std;
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//static members from ConvertChar
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uint8_t ConvertChar::conversionTable[255];
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//Global function pointers in utils.h
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float (*g_compute_full_prob_float)(testcase *tc, float* before_last_log) = 0;
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double (*g_compute_full_prob_double)(testcase *tc, double* before_last_log) = 0;
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//Static members in ContextBase
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bool ContextBase<double>::staticMembersInitializedFlag = false;
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double ContextBase<double>::jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
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double ContextBase<double>::matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
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bool ContextBase<float>::staticMembersInitializedFlag = false;
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float ContextBase<float>::jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
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float ContextBase<float>::matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
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bool is_avx_supported()
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{
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int ecx = 0, edx = 0, ebx = 0;
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__asm__("cpuid"
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: "=b" (ebx),
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"=c" (ecx),
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"=d" (edx)
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: "a" (1)
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);
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return ((ecx >> 28)&1) == 1;
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}
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bool is_sse41_supported()
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{
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int ecx = 0, edx = 0, ebx = 0;
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__asm__("cpuid"
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: "=b" (ebx),
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"=c" (ecx),
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"=d" (edx)
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: "a" (1)
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);
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return ((ecx >> 19)&1) == 1;
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}
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bool is_sse42_supported()
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{
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int ecx = 0, edx = 0, ebx = 0;
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__asm__("cpuid"
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: "=b" (ebx),
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"=c" (ecx),
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"=d" (edx)
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: "a" (1)
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);
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return ((ecx >> 20)&1) == 1;
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}
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uint64_t get_machine_capabilities()
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{
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uint64_t machine_mask = 0ull;
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if(is_avx_supported())
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machine_mask |= (1 << AVX_CUSTOM_IDX);
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if(is_sse42_supported())
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machine_mask |= (1 << SSE42_CUSTOM_IDX);
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if(is_sse41_supported())
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machine_mask |= (1 << SSE41_CUSTOM_IDX);
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return machine_mask;
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}
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void initialize_function_pointers(uint64_t mask)
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{
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//mask = 0ull;
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//mask = (1 << SSE41_CUSTOM_IDX);
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if(is_avx_supported() && (mask & (1<< AVX_CUSTOM_IDX)))
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{
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cout << "Using AVX accelerated implementation of PairHMM\n";
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g_compute_full_prob_float = compute_full_prob_avxs<float>;
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g_compute_full_prob_double = compute_full_prob_avxd<double>;
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}
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else
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if(is_sse41_supported() && (mask & ((1<< SSE41_CUSTOM_IDX) | (1<<SSE42_CUSTOM_IDX))))
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{
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cout << "Using SSE4.1 accelerated implementation of PairHMM\n";
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g_compute_full_prob_float = compute_full_prob_sses<float>;
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g_compute_full_prob_double = compute_full_prob_ssed<double>;
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}
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else
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{
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cout << "Using un-vectorized C++ implementation of PairHMM\n";
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g_compute_full_prob_float = compute_full_prob<float>;
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g_compute_full_prob_double = compute_full_prob<double>;
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}
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}
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int normalize(char c)
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{
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return ((int) (c - 33));
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}
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int read_testcase(testcase *tc, FILE* ifp)
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{
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char *q, *i, *d, *c, *line = NULL;
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int _q, _i, _d, _c;
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int x, size = 0;
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ssize_t read;
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read = getline(&line, (size_t *) &size, ifp == 0 ? stdin : ifp);
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if (read == -1)
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{
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free(line);
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return -1;
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}
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tc->hap = (char *) malloc(size);
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tc->rs = (char *) malloc(size);
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q = (char *) malloc(size);
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i = (char *) malloc(size);
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d = (char *) malloc(size);
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c = (char *) malloc(size);
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if (sscanf(line, "%s %s %s %s %s %s\n", tc->hap, tc->rs, q, i, d, c) != 6)
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return -1;
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tc->haplen = strlen(tc->hap);
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tc->rslen = strlen(tc->rs);
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assert(strlen(q) == tc->rslen);
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assert(strlen(i) == tc->rslen);
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assert(strlen(d) == tc->rslen);
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assert(strlen(c) == tc->rslen);
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//assert(tc->rslen < MROWS);
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//tc->ihap = (int *) malloc(tc->haplen*sizeof(int));
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//tc->irs = (int *) malloc(tc->rslen*sizeof(int));
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tc->q = (char *) malloc(sizeof(char) * tc->rslen);
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tc->i = (char *) malloc(sizeof(char) * tc->rslen);
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tc->d = (char *) malloc(sizeof(char) * tc->rslen);
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tc->c = (char *) malloc(sizeof(char) * tc->rslen);
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for (x = 0; x < tc->rslen; x++)
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{
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_q = normalize(q[x]);
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_i = normalize(i[x]);
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_d = normalize(d[x]);
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_c = normalize(c[x]);
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tc->q[x] = (_q < 6) ? 6 : _q;
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//tc->q[x] = _q;
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tc->i[x] = _i;
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tc->d[x] = _d;
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tc->c[x] = _c;
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//tc->irs[x] = tc->rs[x];
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}
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//for (x = 0; x < tc->haplen; x++)
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//tc->ihap[x] = tc->hap[x];
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free(q);
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free(i);
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free(d);
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free(c);
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free(line);
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return 0;
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}
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unsigned MAX_LINE_LENGTH = 65536;
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int convToInt(std::string s)
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{
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int i;
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std::istringstream strin(s);
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strin >> i;
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return i;
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}
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void tokenize(std::ifstream& fptr, std::vector<std::string>& tokens)
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{
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int i = 0;
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std::string tmp;
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std::vector<std::string> myVec;
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vector<char> line;
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line.clear();
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line.resize(MAX_LINE_LENGTH);
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vector<char> tmpline;
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tmpline.clear();
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tmpline.resize(MAX_LINE_LENGTH);
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myVec.clear();
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while(!fptr.eof())
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{
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i = 0;
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bool still_read_line = true;
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unsigned line_position = 0;
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while(still_read_line)
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{
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fptr.getline(&(tmpline[0]), MAX_LINE_LENGTH);
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if(line_position + MAX_LINE_LENGTH > line.size())
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line.resize(2*line.size());
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for(unsigned i=0;i<MAX_LINE_LENGTH && tmpline[i] != '\0';++i,++line_position)
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line[line_position] = tmpline[i];
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if(fptr.eof() || !fptr.fail())
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{
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still_read_line = false;
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line[line_position++] = '\0';
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}
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}
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std::istringstream kap(&(line[0]));
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while(!kap.eof())
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{
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kap >> std::skipws >> tmp;
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if(tmp != "")
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{
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myVec.push_back(tmp);
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++i;
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//std::cout <<tmp <<"#";
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}
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tmp = "";
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}
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//std::cout << "\n";
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if(myVec.size() > 0)
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break;
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}
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tokens.clear();
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//std::cout << "Why "<<myVec.size()<<"\n";
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tokens.resize(myVec.size());
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for(i=0;i<(int)myVec.size();++i)
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tokens[i] = myVec[i];
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line.clear();
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tmpline.clear();
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}
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int read_mod_testcase(ifstream& fptr, testcase* tc, bool reformat)
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{
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static bool first_call = true;
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vector<string> tokens;
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tokens.clear();
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tokenize(fptr, tokens);
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if(tokens.size() == 0)
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return -1;
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tc->hap = new char[tokens[0].size()+2];
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tc->haplen = tokens[0].size();
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memcpy(tc->hap, tokens[0].c_str(), tokens[0].size());
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tc->rs = new char[tokens[1].size()+2];
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tc->rslen = tokens[1].size();
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tc->q = new char[tc->rslen];
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tc->i = new char[tc->rslen];
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tc->d = new char[tc->rslen];
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tc->c = new char[tc->rslen];
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//cout << "Lengths "<<tc->haplen <<" "<<tc->rslen<<"\n";
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memcpy(tc->rs, tokens[1].c_str(),tokens[1].size());
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assert(tokens.size() == 2 + 4*(tc->rslen));
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//assert(tc->rslen < MROWS);
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for(unsigned j=0;j<tc->rslen;++j)
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tc->q[j] = (char)convToInt(tokens[2+0*tc->rslen+j]);
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for(unsigned j=0;j<tc->rslen;++j)
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tc->i[j] = (char)convToInt(tokens[2+1*tc->rslen+j]);
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for(unsigned j=0;j<tc->rslen;++j)
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tc->d[j] = (char)convToInt(tokens[2+2*tc->rslen+j]);
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for(unsigned j=0;j<tc->rslen;++j)
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tc->c[j] = (char)convToInt(tokens[2+3*tc->rslen+j]);
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if(reformat)
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{
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ofstream ofptr;
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ofptr.open("reformat/debug_dump.txt",first_call ? ios::out : ios::app);
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assert(ofptr.is_open());
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ofptr << tokens[0] << " ";
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ofptr << tokens[1] << " ";
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for(unsigned j=0;j<tc->rslen;++j)
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ofptr << ((char)(tc->q[j]+33));
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ofptr << " ";
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for(unsigned j=0;j<tc->rslen;++j)
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ofptr << ((char)(tc->i[j]+33));
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ofptr << " ";
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for(unsigned j=0;j<tc->rslen;++j)
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ofptr << ((char)(tc->d[j]+33));
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ofptr << " ";
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for(unsigned j=0;j<tc->rslen;++j)
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ofptr << ((char)(tc->c[j]+33));
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ofptr << " 0 false\n";
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ofptr.close();
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first_call = false;
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}
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return tokens.size();
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}
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double getCurrClk() {
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struct timeval tv ;
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gettimeofday(&tv, NULL);
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return (double)tv.tv_sec + (double)tv.tv_usec / 1000000.0;
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}
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inline unsigned long long rdtsc(void)
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{
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unsigned hi, lo;
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__asm__ __volatile__ ("rdtsc" : "=a"(lo), "=d"(hi));
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return ( (unsigned long long)lo)|( ((unsigned long long)hi)<<32 );
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}
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void get_time(struct timespec* store_struct)
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{
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clock_gettime(CLOCK_REALTIME, store_struct);
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}
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uint64_t diff_time(struct timespec& prev_time)
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{
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struct timespec curr_time;
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clock_gettime(CLOCK_REALTIME, &curr_time);
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return (uint64_t)((curr_time.tv_sec-prev_time.tv_sec)*1000000000+(curr_time.tv_nsec-prev_time.tv_nsec));
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}
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#ifdef USE_PAPI
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#include "papi.h"
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#define NUM_PAPI_COUNTERS 4
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#endif
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void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size, bool do_check)
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{
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FILE* fptr = 0;
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ifstream ifptr;
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if(use_old_read_testcase)
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{
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fptr = fopen(filename,"r");
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assert(fptr);
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}
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else
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{
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ifptr.open(filename);
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assert(ifptr.is_open());
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}
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vector<testcase> tc_vector;
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tc_vector.clear();
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testcase tc;
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uint64_t vector_compute_time = 0;
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uint64_t baseline_compute_time = 0;
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uint64_t num_double_calls = 0;
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unsigned num_testcases = 0;
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bool all_ok = do_check ? true : false;
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#ifdef USE_PAPI
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uint32_t all_mask = (0);
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uint32_t no_usr_mask = (1 << 16); //bit 16 user mode, bit 17 kernel mode
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uint32_t no_kernel_mask = (1 << 17); //bit 16 user mode, bit 17 kernel mode
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PAPI_num_counters();
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int events[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
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char* eventnames[NUM_PAPI_COUNTERS]= { "cycles", "itlb_walk_cycles", "dtlb_load_walk_cycles", "dtlb_store_walk_cycles" };
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assert(PAPI_event_name_to_code("UNHALTED_REFERENCE_CYCLES:u=1:k=1",&(events[0])) == PAPI_OK);
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assert(PAPI_event_name_to_code("ITLB_MISSES:WALK_DURATION", &(events[1])) == PAPI_OK);
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assert(PAPI_event_name_to_code("DTLB_LOAD_MISSES:WALK_DURATION", &(events[2])) == PAPI_OK);
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assert(PAPI_event_name_to_code("DTLB_STORE_MISSES:WALK_DURATION", &(events[3])) == PAPI_OK);
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long long values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
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long long accum_values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
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#endif
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while(1)
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{
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int break_value = use_old_read_testcase ? read_testcase(&tc, fptr) : read_mod_testcase(ifptr,&tc,true);
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if(break_value >= 0)
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tc_vector.push_back(tc);
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if(tc_vector.size() == BATCH_SIZE || (break_value < 0 && tc_vector.size() > 0))
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{
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vector<double> results_vec;
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vector<double> baseline_results_vec;
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results_vec.clear();
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baseline_results_vec.clear();
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results_vec.resize(tc_vector.size());
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baseline_results_vec.resize(tc_vector.size());
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struct timespec start_time;
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#ifdef USE_PAPI
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assert(PAPI_start_counters(events, NUM_PAPI_COUNTERS) == PAPI_OK);
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#endif
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get_time(&start_time);
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#pragma omp parallel for schedule(dynamic,chunk_size) num_threads(12)
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#ifdef DO_REPEAT_PROFILING
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for(unsigned z=0;z<10;++z)
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#endif
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{
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for(unsigned i=0;i<tc_vector.size();++i)
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{
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testcase& tc = tc_vector[i];
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float result_avxf = g_compute_full_prob_float(&tc, 0);
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double result = 0;
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if (result_avxf < MIN_ACCEPTED) {
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double result_avxd = g_compute_full_prob_double(&tc, 0);
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result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
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++num_double_calls;
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}
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else
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result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
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#ifdef DUMP_COMPUTE_VALUES
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g_load_time_initializer.debug_dump("return_values_vector.txt",to_string(result),true);
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#endif
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results_vec[i] = result;
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}
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}
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#ifdef USE_PAPI
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assert(PAPI_stop_counters(values, NUM_PAPI_COUNTERS) == PAPI_OK);
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#endif
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vector_compute_time += diff_time(start_time);
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#ifdef USE_PAPI
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for(unsigned k=0;k<NUM_PAPI_COUNTERS;++k)
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accum_values[k] += values[k];
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#endif
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num_testcases += tc_vector.size();
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if(do_check)
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{
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get_time(&start_time);
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#pragma omp parallel for schedule(dynamic,chunk_size)
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for(unsigned i=0;i<tc_vector.size();++i)
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{
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testcase& tc = tc_vector[i];
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double baseline_result = compute_full_prob<double>(&tc);
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baseline_result = log10(baseline_result) - log10(ldexp(1.0, 1020.0));
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baseline_results_vec[i] = baseline_result;
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}
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baseline_compute_time += diff_time(start_time);
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for(unsigned i=0;i<tc_vector.size();++i)
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{
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double baseline_result = baseline_results_vec[i];
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double abs_error = fabs(baseline_result-results_vec[i]);
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double rel_error = (baseline_result != 0) ? fabs(abs_error/baseline_result) : 0;
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if(abs_error > 1e-5 && rel_error > 1e-5)
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{
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cout << std::scientific << baseline_result << " "<<results_vec[i]<<"\n";
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all_ok = false;
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}
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}
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}
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for(unsigned i=0;i<tc_vector.size();++i)
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{
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delete tc_vector[i].rs;
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delete tc_vector[i].hap;
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delete tc_vector[i].q;
|
|
delete tc_vector[i].i;
|
|
delete tc_vector[i].d;
|
|
delete tc_vector[i].c;
|
|
}
|
|
results_vec.clear();
|
|
tc_vector.clear();
|
|
}
|
|
if(break_value < 0)
|
|
break;
|
|
}
|
|
#ifdef DUMP_COMPUTE_VALUES
|
|
g_load_time_initializer.debug_close();
|
|
#endif
|
|
if(all_ok)
|
|
{
|
|
cout << "All output values within acceptable error\n";
|
|
cout << "Baseline double precision compute time "<<baseline_compute_time*1e-9<<"\n";
|
|
}
|
|
cout << "Num testcase "<<num_testcases<< " num double invocations "<<num_double_calls<<"\n";
|
|
cout << "Vector compute time "<< vector_compute_time*1e-9 << "\n";
|
|
#ifdef USE_PAPI
|
|
for(unsigned i=0;i<NUM_PAPI_COUNTERS;++i)
|
|
cout << eventnames[i] << " : "<<accum_values[i]<<"\n";
|
|
#endif
|
|
|
|
if(use_old_read_testcase)
|
|
fclose(fptr);
|
|
else
|
|
ifptr.close();
|
|
}
|